In the present study, a novel sample preparation method based on magnetic core-mesoporous shell microspheres with C8-modified interior pore walls (C8-Fe3O4@mSiO2) was established for the identification of 20(S)-protopanaxadiol (PPD) metabolites in rat plasma by UPLC-Q-TOF-MS/MS analysis. C8-Fe3O4@mSiO2 allowed selective extraction of PPD metabolites from rat plasma by excluding macromolecules in the plasma owing to size exclusion effect. Five extraction conditions including the amount of C8-Fe3O4@mSiO2 microspheres used, extraction time, elution solvents, elution volume, and elution time were investigated and optimized. The present method was compared with two conventional sample preparation methods: protein precipitation and C8 solid phase extraction (C8-SPE). Our method provided higher UPLC intensity of result than protein precipitation method. While the resulting intensity of our method and that of C8-SPE were not significantly different, it consumed less processing time (15min 55s for C8-Fe3O4@mSiO2, and 27min 30s for C8-SPE). Finally, the proposed method was successfully applied in the identification of PPD metabolites in vivo, in which a total of 17 metabolites and the parent drug were identified in rat plasma.